A target consists of three role performing components; adapter, board and microcontroller unit (MCU). The adapter role, often performed by a JTAGICE mkII, communicates with the MCU and is responsible for executing the programming and/or debugging commands. The board is the hardware where the MCU is mounted, and may contain external memory which can be used by the MCU.
The easiest way of adding a target is to use the Scan Targets action. Open the "AVR32 Targets view" and right click in it. This will bring up the view context menu. Select the action and let it discover whatever devices you have plugged into the USB port. If you have a JTAGICE mkII it will be shown here.
If no target was discovered you can manually add a new one by pressing the Add target tool button in the view.
Select the target that was just discovered and press Enter. This will open up the properties view for the target. If the target was added manually you must select the Details tab and set the correct debugger/programmer.
It is not required to specify a Board unless external memory is being used.
Target management is done trough the target view.